I've got a friend that's somewhat interested in doing Stronglifts, but for personal reasons she's utterly terrified of tearing up her knees from doing squats. I've tried to convince her otherwise but to no avail. Is there another exercise, or group of exercises, that can replace a squat? Or even a modified squat that's a lot easier on the knees?

Did she read the StrongLifts PDF that has about fifteen pages dedicated to why squats are both essential and safe? If she's convinced by anecdote, that should do it. If she's more convinced by science, point her to this instead.
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Dave LiepmannAug 14 '12 at 13:44

6 Answers
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The exercise famous for being hard on the knees is the leg press - not squat. If the squat is done with the correct depth (hip lower than the knee) so that the change of direction is NOT done while the knees are at right angles, it shouldn't hurt the knees. If you get some soft knee wraps you might be able to convince her to squat with those.

If not - I would highly recommend lunges holding dumbbells. They train similar muscles.

IMO leg extensions are even worse, and have even less real-world value. The leg press is easier on the back than weighted squats, but has very similar potential for causing knee issues. It's the turn-around that over-stresses the joint. Deadlifts can be very similar to squats, have a smaller ROM, and don't have a weighted turn-around point if you put the weight on the floor.
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Dave NewtonAug 14 '12 at 12:58

@DaveNewton What do you mean by turn-around point?
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Dave LiepmannAug 14 '12 at 13:46

@DaveLiepmann The point at which the squat reverses direction.
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Dave NewtonAug 14 '12 at 14:02

@DaveNewton I'd +1 your comment except for "the turn-around over-stresses the joint". Squats stress and thereby strengthen the joint, but my understanding of the research (for instance) is that the joint is protected during that phase (and throughout the movement, properly performed).
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Dave LiepmannAug 14 '12 at 15:30

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The question is where the forces are coming from. Past parallel, the hamstrings and calves are engaged, pulling the knee from behind during the direction change. This counterbalances the force applied to the anterior side during descent. While ascent is occuring, primary movers are the posterior chain. This in affect removes the worst of the forces from the joint itself. As opposed to never going low enough to engage the posterior chain. The knee would then not have the counterbalance forces to control the stress.
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Berin LoritschAug 14 '12 at 17:08

I will say that I have had more stress on my knees from martial arts training than I ever had from heavy squats. The book Starting Strength has some good information on why this is. The important and critical factor is getting the hips below the knees before changing directions.

The depth causes certain things to happen that protect the knees:

Posterior chain is engaged, providing a counterbalance from behind the knee

Gluteous muscles are engaged to initiate the lift out of the bottom

Knees are traveling in ergonomic paths (assuming toes and knees are aligned in the same direction)

The forces are distributed to larger muscles that are able to bear the stress rather than the joint itself.

The bottom line is that there is no lift that can adequately replace squats. Lunges are acceptable, but if you are worried about knee health the idea of touching the knee to the floor with weights is not really appealing. Goblet squats are a good way to get introduced to the movement, get some torso strength, and more easily get to depth.

Running, partial squats, jumps, etc. are all exercises that place much higher stresses on the knee joint. One of the main factors is the fact that only the anterior muscles are engaged when you land. The force imparted to the knee as your weight is coming down and your foot is already on the immovable earth is up to 3x your body weight. The impact is much faster than it would be to get the posterior chain involved--thus no help. Squats protect your knee, and help improve your posterior chain use even in these high stress activities. As long as all the forces come from one side of your body (anterior chain or posterior chain), there is an increased risk of injury. When both sides of your body are engaged, the load is distributed to the muscle rather than the joints.

We will lose this argument

Let's assume you're not going to convince her that squats are good for her knees. They are, but you can only lead a horse to water. What, then, should you have her do instead?

First, get the idea of StrongLifts out of your head. If you're not squatting, you're not doing StrongLifts. It's essential to programs like this to squat heavy three times a week. In fact, on page 41 of the StrongLifts ebook, it says:

Squats are the most important exercise of StrongLifts 5x5.

So doing "StrongLifts" without squats is out of the question. She can do a linear progression on everything else if she wants.

Substitutes

You could have her do goblet squats until she gets her big girl pants on and realizes that real squats are what strong and healthy people do. Not everybody has to do a 3-times-a-week back squats in order to live their life healthfully. (But it sure helps.) Sometimes just "not weak" is enough. Goblet squats can do that. Unfortunately, they might trigger the same danger signals she has for barbell squats.

Lunges would be great. Here's what I'd try: have her do lunges with dumbbells--heavy dumbbells, no five pound BS--and stick with that for a few workouts. Increase the weight as possible. If she's okay with that after a few weeks, spring this question on her: why is bending her knee for a lunge safe, but bending her knee for a squat dangerous? If someone is convinceable, that should work. If they're not, well, fine. We must open our arms to the gentle indifference of the world.

Air squats, adding weight at an imperceptible pace with the wimpy dumbbells until she's doing real work, might weasel past her anti-squat defenses and get her to do real work. It's worth a try.

But it's very possible that she'll reject these and all other fruitful substitutes for barbell back squats (e.g. pistol squats, Bulgarian split squats, front squats...). The problem is that for the substitute to work, it needs to bend the knees deeply. Since she's terrified of using her knees for the purpose which they evolved for--bending deeply--it's kind of a problem. So we might not be able to substitute anything for squats.

Alternatives

So now we're not doing StrongLifts, and we're not squatting or lunging. What are we left with in a world without squatting?

Lift heavy some other way. Focus on deadlifts, heavy presses, and getting to a set of real pull-ups. Lift heavy. Drag a sled and sprint. Maybe throw in a couple farmer's walks--as heavy as humanly possible--since you have time in your workout now that squats are forbidden. Lift heavy.

Linear progression is king, but if someone is scared of squatting I have doubts that they'll add five pounds to their bench press every session. It might be necessary to scale back the progression to add weight every other workout or even less frequently.

You'll never replace the squats, but if she lifts heavy in every other way, it probably won't be a big deal.

Is there another exercise, or group of exercises, that can replace a
squat?

The squat is the only strength training exercise that involves a pattern known as "hip drive." The hip drive is essentially recruitment of the muscles in the posterior chain--hamstrings, glutes, adductors. You could individually target each muscle, however that would be inefficient as the body is designed to work as a whole, so the focus should be on compound exercises that trains the muscle groups.

In fact, squats are considered by most to be the "grandfather" of all strength training exercises--that is how important they are.

for personal reasons she's utterly terrified of tearing up her knees
from doing squats

She shouldn't be. Squats are a natural human movement, and even babies squat below parallel (albeit without a barbell on their shoulders). If the squat was so dangerous, you wouldn't see babies doing it, and you certainly wouldn't see so many strength training programs advocating its use.

Performed correctly, a squat can potentially rehabilitate the knees... not destroy them. Personally speaking, I have bad knees, and I noticed a definite improvement once I started squatting; I just had to ensure that I maintained good form. If she is concerned with form, I recommend buying the book Starting Strength--Basic Barbell Training. It helps tremendously. Another route would be to upload videos to strength training websites for form checks (i.e. the stronglifts.com forum).

And KB swings. But "even babies squat below parallel" is a bit of a red herring; babies can also put their feet behind their heads, but if you ask the majority of adults to do the same, make a wish first and hope you get the bigger piece. Squats, done correctly, and following a progression if you're deconditioned, are safe--no disagreement there.
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Dave NewtonAug 14 '12 at 15:41

Dave#1: they don't fully activate the posterior chain as squats do, assuming you are doing below parallel back squats. #Dave2: it was more of an anecdotal piece than anything, and yeah, the Law of Individual Differences says your mileage may vary. But as you said, fishy herrings aside, the squats are quite safe for use.
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MosesAug 14 '12 at 17:12

@Moses It's not sufficient cause for a downvote, but I don't understand how a deadlift (or clean, or sprint, or hip thrust, or any other hip-extension exercise) doesn't sufficiently load or activate the posterior chain.
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Dave LiepmannAug 14 '12 at 21:05

@DaveLiepmann the posterior chain is made up of multiple muscle groups, and each of those exercises fails to properly engage 1 or more of those muscles groups. In the case of the deadlift, it does not have a large enough range of motion and it does not fully engage the adductors. The deadlift gives the glutes and hamstrings a massive workout, dont get me wrong, it just doesn't fully engage the posterior chain as I said before.
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MosesAug 15 '12 at 2:08

If she is "terrified" that she will tear up her knees with the squat, she very likely will. She probably has (or had) a significant knee problem. Even if she doesn't have knee problems, trying to do an exercise while in a state of fear can affect one's tension, attention and form.

If she has knee problems:

My suggestion would be to strengthen the glutes without involving the knees using levers or cables. This bodyweight could also be ok, depending on the knee problem. If she does have a knee problem, strengthening the glutes will help reduce strain on the knees. If/as her knees improve from increased glute strength, she may be more likely to want to try squats, esp. given all the information included in other answers as to why squats can help strengthen the knees.

The beauty of the squat however is that it targets many of the body's large muscle groups so you would also have to consider the trunk muscles (front, back and sides - planks, side planks etc.) and calves.

If she doesn't have knee problems and it is just the idea of a squat with weight that scares her, kettlebell swings may be a helpful alternative.

As she gets stronger with other exercises she may feel more confident to try the squat. Also, when she realizes how many exercises you need to do to equal one squat, she may decide that the squat is worth learning.

Consider deadlifts (not the stiff-legged ones); they have a small range-of-motion, and don't weight the turn-around point if the weight is set on the floor. (Or reduce rep speed, particularly at turn-around.)

Without knowing what the "personal reasons" are it's difficult to provide actionable advice, however, because only exercises that target the same muscles, hence the same joint, will have similar effects.

It's also possible to progress into weighted squats after building up strength and connective tissues through body-weight squats. Depending on her goals, they may be enough on their own anyway.

Deadlifts are already in the StrongLifts program. Would you suggest she add more sets of them, do them heavier, do a variant, or just omit squats?
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Dave LiepmannAug 14 '12 at 13:45

@DaveLiepmann Hard to say since there aren't any details regarding the squatting issue. I don't think omitting them would be all that horrible. I'm reluctant to encourage them without knowing the reason she wants to avoid them, although healthy knees should be able to handle them, especially with a long ramp-up period.
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Dave NewtonAug 14 '12 at 14:04